Distribution of volume, microvoid percolation, and packing density in globular proteins

TL;DR

This paper introduces a fast grid-based method to analyze volume, microvoid percolation, and packing density in globular proteins, revealing that packing density is uniform and size-independent within these proteins.

Contribution

A novel, efficient grid-based approach for characterizing volume and void distribution in proteins, linking microvoid volume to percolation theory and clarifying packing density discrepancies.

Findings

Packing density is spatially uniform in globular proteins.

Microvoid volume analysis explains previous discrepancies in packing density.

Model parameterization aligns with experimental data, confirming size independence.

Abstract

A fast and accurate grid-based method with low memory requirement is presented to calculate volume characteristics in molecular systems. The distribution of volume and packing density is characterized in globular proteins, where void space is decomposed into microvoid volume and cavities based on a spherical test probe with variable radius. A scan over test probe radius is mapped onto a site percolation problem for microvoid volume. Finite-size scaling is applied to determine critical exponents, which are found to be consistent with connectivity percolation exponents in three dimensions. Disparate results in the literature regarding packing density in the core of a protein compared to on its surface, and with respect to protein size, is elucidated in terms of microvoid volume within a unified implicit-solvent model. By parameterizing the model to match the results of explicit-solvent models that agree with experimental data, we verify that packing density within globular proteins is spatially uniform and independent of protein size.